BioGrids installation client - Usage

All BioGrids software is run from the the terminal.
For information on how to run software from the BioGrids collection and configure your shell, check the getting started page..

General

The BioGrids software installation client is a command line-based installer for the BioGrids software collection. The application allows for selected applications to be installed in the familiar BioGrids environment.

To get started, load the BioGrids environment :

$ source /programs/biogrids.shrc

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Software Support by BioGrids
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Developed with support from HMS Tools-and-Technologies fund.
If your use of BioGrids compiled software was an important element in
your publication, please include the following statement in your work:
"Software used in the project was installed and configured by BioGrids
(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"
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This BioGrids installation last updated: 2017-10-11
Please submit bug reports and help requests to: help@biogrids.org.
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Capsule Status: Active
For additional information visit https://sbgrid.org/wiki/capsules
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### Version selection
Default versions are installed for each application. BioGrids makes available several versions for each software package. You can install specific versions if needed.
To do so, specify the version after the title name with an @ symbol. Use the *biogrids info <title>* command to see all available versions.
$ biogrids info samtools

Package: SAMtools
Name slug: samtools

Available versions:
* 0.1.19
* 1.3
* 1.3.1
* 1.4.1
* 1.5 (default)

Grids(s): Biogrids
Collection(s): High-Throughput Sequencing

Description:
(Sequence Alignment/Map) a generic format for storing large nucleotide
sequence alignments that provides various utilities for manipulating
alignments, including sorting, merging, indexing and generating alignments
in a per-position format.

Software Version Management in the BioGrids environment

If you have a single version of an application installed, explicit version selection in your environment is not needed.

In the case of multiple installed versions, the BioGrids Default version will be the version available at the terminal when it is installed, unless configured otherwise in ~/.sbgrid.conf.

In the case of multiple non-default versions installed, the latest release will be the version available in your shell. If you would like to have more than one version of a title installed, and prefer to use an older release or the non-default version when a default version is installed, you must set this explicitly in your ~/.sbgrid.conf file. This is the same as in the standard BioGrids environment.

Running BioGrids software

To use the software at the terminal in bash, open a new terminal and run

$ source /programs/biogrids.shrc

or in tcsh

$ source /programs/biogrids.cshrc

Questions, Problems and Known Issues

For questions or problems, the Help menu will direct you to the BioGrids help page. Or just email help@biogrids.org.
If relevant, please include a screenshot of the GUI if possible (command + shift + 4) and please include the ~/Library/Application Support/BioGrids/biogrids.log file with your report.

Known issues

The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

In some cases the prompt for admin credentials fails to appear on activation. Be sure there is no prior BioGrids install on your machine at /programs or /opt/biogrids.